GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
Daniel Cameron(The University of Melbourne), Jonathan Baber(Hartwig Medical Foundation), Charles Shale(Hartwig Medical Foundation), Jose Espejo Valle-Inclán(Heidelberg University), Nicolle Besselink(Heidelberg University), Arne van Hoeck(Heidelberg University), Roel Janssen(Heidelberg University), Edwin Cuppen(Heidelberg University), Peter Priestley(Hartwig Medical Foundation), Anthony T. Papenfuss(The University of Melbourne)
Cited by 190Open Access
Abstract
GRIDSS2 is the first structural variant caller to explicitly report single breakends-breakpoints in which only one side can be unambiguously determined. By treating single breakends as a fundamental genomic rearrangement signal on par with breakpoints, GRIDSS2 can explain 47% of somatic centromere copy number changes using single breakends to non-centromere sequence. On a cohort of 3782 deeply sequenced metastatic cancers, GRIDSS2 achieves an unprecedented 3.1% false negative rate and 3.3% false discovery rate and identifies a novel 32-100 bp duplication signature. GRIDSS2 simplifies complex rearrangement interpretation through phasing of structural variants with 16% of somatic calls phasable using paired-end sequencing.